Biology subjects

wang, x.

Publications and source records attributed to wang, x..

26 records · Page 2Linked to original sources

bioRxiv2020

The Rhinolophus affinis bat ACE2 and multiple animal orthologs are functional receptors for bat coronavirus RaTG13 and SARS-CoV-2

Bat coronavirus (CoV) RaTG13 shares the highest genome sequence identity with SARS-CoV-2 among all known coronaviruses, and also uses human angiotensin converting enzyme 2 (hACE2) for virus entry. Thus, SARS-CoV-2 is thought to have originated from bat. However, whether SARS-CoV-2 emerged from bats directly or through an intermediate host remains elusive. Here, we found that Rhinolophus affinis bat ACE2 (RaACE2) is an entry receptor for both SARS-CoV-2 and RaTG13, although RaACE2 binding to the receptor binding domain (RBD) of SARS-CoV-2 is markedly weaker than that of hACE2. We further evaluated the receptor activities of ACE2s from additional 16 diverse animal species for RaTG13, SARS-CoV, and SARS-CoV-2 in terms of S protein binding, membrane fusion, and pseudovirus entry. We found that the RaTG13 spike (S) protein is significantly less fusogenic than SARS-CoV and SARS-CoV-2, and seven out of sixteen different ACE2s function as entry receptors for all three viruses, indicating that all three viruses might have broad host rages. Of note, RaTG13 S pseudovirions can use mouse, but not pangolin ACE2, for virus entry, whereas SARS-CoV-2 S pseudovirions can use pangolin, but limited for mouse, ACE2s enter cells. Mutagenesis analysis revealed that residues 484 and 498 in RaTG13 and SARS-CoV-2 S proteins play critical roles in recognition of mouse and human ACE2. Finally, two polymorphous Rhinolophous sinicus bat ACE2s showed different susceptibilities to virus entry by RaTG13 and SARS-CoV-2 S pseudovirions, suggesting possible coevolution. Our results offer better understanding of the mechanism of coronavirus entry, host range, and virus-host coevolution.

microbiology↗

bioRxiv2020

Introduction of a precocious metamorphosis BmNPV infection in the latter half of the fifth instar silkworm larvae

The silkworm, Bombyx mori, is a complete metamorphosis insect, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. This study performed a transcriptome analysis of silkworm PGs after BmNPV infection. Transcriptome data were annotated with KEGG, GO, and shown to be of high quality by RT-qPCR. The spatial expression profiles of BmJing and BmAryl indicate that they may be specifically expressed in silkworm PGs. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected larvae at 24, 48, and 72 h and at the developmental stages of days-6 and 7, comparing to day-3, reveal that the DEGs may be related to the BmNPV infection via promoting early maturation in the latter half of the silkworm fifth instar. This study is the first report on the identification of possible genes in PGs correlating with the precocious molting and metamorphosis of silkworm larvae under BmNPV infection in the latter half of the fifth instar. Our findings will help to address the interactions between BmNPV infection and host developmental response. This work provides a new perspective on BmNPV infection and host developmental response, as well as suggesting candidate genes for further research.

molecular biology↗

bioRxiv2020

Therapeutic role of recurrent ESR1-CCDC170 gene fusions in breast cancer endocrine resistance

Background Endocrine therapy is the most common treatment for estrogen receptor (ER)-positive breast cancer, but its effectiveness is limited by high rates of primary and acquired resistance. There are likely many genetic causes and recent studies suggest the important role of ESR1 mutations and fusions in endocrine resistance. Previously we reported a recurrent ESR1 fusion called ESR1-CCDC170 in 6-8% of the luminal B breast cancers that has a worse clinical outcome after endocrine therapy. Despite being the most frequent ESR1 fusion, its functional role in endocrine resistance have not been studied in vivo, and the engaged mechanism and therapeutic relevance remain uncharacterized.Methods The endocrine sensitivities of HCC1428 or T47D breast cancer cells following genetic perturbations of ESR1-CCDC170 were assessed using clonogenic assays and/or xenograft mouse models. The underlying mechanisms were investigated by reverse phase protein array, western blotting, immunoprecipitation, and bimolecular fluorescence complementation assays. The sensitivity of ESR1-CCDC170 expressing breast cancer cells to concomitant treatments of tamoxifen and HER/SRC inhibitors was assessed by clonogenic assays.Results Our results suggested that different ESR1-CCDC170 fusions endow different levels of reduced endocrine sensitivity in vivo, resulting in significant survival disadvantages. Further investigation revealed a novel mechanism that ESR1-CCDC170 binds to HER2/HER3/SRC and activates SRC/PI3K/AKT signaling. Silencing of ESR1-CCDC170 in the fusion-positive cell line, HCC1428, downregulates HER2/HER3, represses pSRC/pAKT, and improves endocrine sensitivity. More important, breast cancer cells expressing ectopic or endogenous ESR1-CCDC170 are highly sensitive to treatment regimens combining endocrine agents with the HER2 inhibitor lapatinib and/or the SRC inhibitor dasatinib.Conclusion ESR1-CCDC170 may endow breast cancer cell survival under endocrine therapy via maintaining/activating HER2/HER3/SRC/AKT signaling which implies a potential therapeutic strategy for managing these fusion positive tumors.Competing Interest StatementDr. Rachel Schiff receives research funding from AstraZeneca, GlaxoSmithKline, Gilead Sciences, and PUMA Biotechnology, outside of this project; and is a consulting/advisory committee member for Macrogenics, and Eli Lilly. The other coauthors do not have competing financial interests.AbbreviationsABCATP-binding cassetteAIsaromatase inhibitorsBiFCBimolecular Fluorescence ComplementationCCDC170coiled-coil domain containing 170CSScharcoal-stripped serumΔCCDC170truncated CCDC170 proteinsE2estradiolERestrogen receptorFDAFood and Drug Administration4-OHT4-hydroxytamoxifenORFopen reading frameRPPAReverse phase protein array analysisSERDsselective ER down-regulatorsSERMsselective ER modulatorssiRNAsmall interfering RNASMCstructural maintenance of chromosomesTPERTissue Protein Extraction ReagentView Full Text

cancer biology↗

bioRxiv2020

Single cell chromatin accessibility of the developmental cephalochordate

The phylum chordata are composed of three groups: vertebrata, tunicate and cephalochordata. Single cell developmental atlas for typical species in vertebrata (mouse, zebrafish, western frog, worm) and tunicate (sea squirts) has been constructed recently. However, the single cell resolution atlas for lancelet, a living proxy of vertebrate ancestors, has not been achieved yet. Here, we profiled more than 57 thousand cells during the development of florida lancelet (Branchiostoma floridae), covering important processes including embryogenesis, organogenesis and metamorphosis. We identified stage and cluster specific regulatory elements. Additionally, we revealed the regulatory codes underlying functional specification and lineage commitment. Based on epigenetic features, we constructed the developmental trajectory for lancelet, elucidating how cell fates were established progressively. Overall, our study provides, by far, the first single cell regulatory landscape of amphioxus, which could help us to understand the heterogeneity and complexity of lancet development at single cell resolution and throw light upon the great transition from simple chordate ancestor to modern vertebrates with amazing diversity and endless forms.

developmental biology↗

bioRxiv2019

SK4 calcium-activated potassium channels activated by sympathetic nerves enhances atrial fibrillation vulnerability in a canine model of acute stroke

New-onset atrial fibrillation (AF) is common in patients with acute stroke (AS). Studies have shown that intermediate-conductance KCa channels (SK4) play an important role in cardiomyocyte automaticity. The aim of this study was to investigate the effects of SK4 on AF vulnerability in dogs with AS. Eighteen dogs were randomly divided into a control group, AS group and left stellate ganglion ablation (LSGA) group. In the control group, dogs received craniotomy without right middle cerebral artery occlusion (MCAO). AS dogs were established using a cerebral ischemic model with right MCAO. LSGA dogs underwent MCAO, and LSGA was performed. Three days later, the dispersion of the effective refractory period (dERP) and AF vulnerability in the AS group were significantly increased compared with those in the control group and LSGA group. However, no significant difference in dERP and AF vulnerability was found between the control group and the LSGA group. The SK4 inhibitor (TRAM-34) completely inhibited the inducibility of AF in AS dogs. SK4 expression and levels of noradrenaline (NE), {beta}1-AR, p38 and c-Fos in the atrium were higher in the AS dogs than in the control group or LSGA group. However, no significant difference in SK4 expression or levels of NE, {beta}1-AR, p38 and c-Fos in the left atrium was observed between the control group and LSGA group. SK4 plays a key role in AF vulnerability in a canine model with AS. The effects of LSGA on AF vulnerability were associated with the p38 signaling pathways.

neuroscience↗

bioRxiv2019

IL-10 Promotes Endothelial Progenitor Cell Driven Wound Neovascularization and Enhances Healing via STAT3.

Evidence from prior studies of cutaneous trauma, burns, and chronic diabetic wound repair demonstrates that endothelial progenitor cells (EPCs) contribute to de novo angiogenesis, anti-inflammatory reactions, tissue regeneration, and remodeling. We have shown that IL-10, a potent anti-inflammatory cytokine, promotes regenerative tissue repair in an adult model of dermal scar formation via the regulation of fibroblast-specific hyaluronan synthesis in a STAT3 dependent manner. While it is known that IL-10 drives EPC recruitment and neovascularization after myocardial infarction, its specific mode of action, particularly in dermal wound healing and neovascularization in both control and diabetic wounds remains to be defined. Here we show that IL-10 promotes EPC recruitment into the dermal wound microenvironment to facilitate neovascularization and wound healing of control and diabetic (db/db) wounds via vascular endothelial growth factor (VEGF) and stromal-cell derived factor 1 (SDF-1) signaling. Inducible skin-specific STAT3 knockout (KO) mice were studied to determine whether the impact of IL-10 on the neovascularization and wound healing is STAT3 dependent. We found that IL-10 treatment significantly promotes dermal wound healing with enhanced wound closure, robust granulation tissue formation and neovascularization. This was associated with elevated wound EPC counts as well as increased VEGF and high SDF-1 levels in control mice, an effect that was abrogated in STAT3 KO transgenic mice. These findings were supported in vitro, wherein IL-10-enhanced VEGF and SDF-1 synthesis in primary murine dermal fibroblasts. IL-10-conditioned fibroblast media was shown to promote sprouting and network formation in aortic ring assays. We conclude that overexpression of IL-10 in the wound-specific milieu recruits EPCs and promote neovascularization, which occurs in a STAT3-dependent manner via regulation of VEGF and SDF-1 levels. Collectively, our studies demonstrate that IL-10 increases EPC recruitment leading to enhanced neovascularization and healing of dermal wounds.

physiology↗

bioRxiv2019

An Optimally Weighted Combination Method to DetectNovel Disease Associated Genes Using Publicly Available GWAS Summary Data

Gene-based analyses offer a useful alternative and complement to the usual single nucleotide polymorphism (SNP) based analysis for genome-wide association studies (GWASs). Using appropriate weights (pre-specified or eQTL-derived) can boost statistical power, especially for detecting weak associations between a gene and a trait. Because the sparsity level or association directions of the underlying association patterns in real data are often unknown and access to individual-level data is limited, we propose an optimal weighted combination (OWC) test applicable to summary statistics from GWAS. This method includes burden tests, weighted sum of squared score (SSU), weighted sum statistic (WSS), and the score test as its special cases. We analytically prove that aggregating the variants in one gene is the same as using the weighted combination of Z-scores for each variant based on the score test method. We also numerically illustrate that our proposed test outperforms several existing comparable methods via simulation studies. Lastly, we utilize schizophrenia GWAS data and a fasting glucose GWAS meta-analysis data to demonstrate that our method outperforms the existing methods in real data analyses. Our proposed test is implemented in the R program OWC, which is freely and publicly available.

genetics↗

bioRxiv2019

A General Statistic to Test an Optimally WeightedCombination of Common and/or Rare Variants

Both genome-wide association study and next generation sequencing data analyses are widely employed in order to identify disease susceptible common and/or rare genetic variants in many large scale genetic studies. Rare variants generally have large effects though they are hard to detect due to their low frequency. Currently, many existing statistical methods for rare variants association studies employ a weighted combination scheme, which usually puts subjective weights or suboptimal weights based on some ad hoc assumptions (e.g. ignoring dependence between rare variants). In this study, we analytically derive optimal weights for both common and rare variants and propose a General and novel approach to Test association between an Optimally Weighted combination of variants (G-TOW) in a gene or pathway for a continuous or dichotomous trait while easily adjusting for covariates. We conduct extensive simulation studies to evaluate the performance of G-TOW. Results of the simulation studies show that G-TOW has properly controlled type I error rates and it is the most powerful test among the methods we compared, when testing effects of either both rare and common variants or rare variants only. We also illustrate the effectiveness of G-TOW using the Genetic Analysis Workshop 17 (GAW17) data. In addition, we applied G-TOW and other competitive methods to test association for schizophrenia. The G-TOW have successfully verified genes FYN and VPS39 which are associated with schizophrenia reported in existing publications. Both of these genes are missed by the weighted sum statistic (WSS) and the sequence kernel association test (SKAT). G-TOW also showed much stronger significance (p-value=0.0037) than our previously developed method named Testing the effect of an Optimally Weighted combination of variants (TOW) (p-value=0.0143) on gene FYN. FYN is a member of the protein-tyrosine kinase oncogene family that phosphorylates glutamate metabotropic receptors and ionotropic N-methyl-d-aspartate (NMDA) receptors. NMDA modulates trafficking, subcellular distribution and function. It is involved in neuronal apoptosis, brain development and synaptic transmission and lower expression, which has been observed in the platelets of schizophrenic patients compared with controls. The application for schizophrenia indicates that G-TOW is a powerful tool in genome-wide association studies.

genetics↗